Bacterial Argonaute proteins aid cell division in the presence of topoisomerase inhibitors in Escherichia coli
Abstract
Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix roseae (LrAgo) act as DNA-guided DNA nucleases in Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin. Both pAgos are preferentially loaded with small DNA guides derived from the sites of replication termination. The amount of pAgo-associated small DNAs (smDNAs) from the termination sites is increased in the presence ciprofloxacin, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin also enhances asymmetry in the distribution of smDNAs around Chi-sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases help to complete replication of chromosomal DNA by targeting the sites of termination, and may switch their functional activities when expressed in different host species.
Additional Information
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. We thank Daria Esyunina for continued advice on this study, Phillip Zamore, Samson M. Jolly and Dmitry Sutormin for helpful discussions. This work was supported by grant 19-14-00359 of the Russian Science Foundation to Daria Esyunina. The authors declare no competing interests. AUTHOR CONTRIBUTIONS. Andrey Kulbachinskiy and Alexei Aravin conceived the study, Anna Olina performed experiments, Aleksei Agapov performed bioinformatic analysis of small DNA libraries, Denis Yudin made the original discovery of the chromosomal specificity of pAgos under supervision of Anton Kuzmenko and performed initial analysis of small DNAs, Anna Olina and Aleksei Agapov prepared the figures, Andrey Kulbachinskiy wrote the manuscript with contributions from all the authors. DATA AVAILABILITY. The smDNA sequencing datasets generated in this study are available from the Sequence Read Archive (SRA) database under bioproject number PRJNA878808. The code used for data analysis is available at the GitHub repository at https://github.com/AlekseiAgapov/SeAgo_LrAgo. All primary data are available from the corresponding author upon request.Attached Files
Submitted - 2022.09.13.507849v2.full.pdf
Supplemental Material - media-1.pdf
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Additional details
- Eprint ID
- 120333
- Resolver ID
- CaltechAUTHORS:20230322-367204000.18
- 19-14-00359
- Russian Science Foundation
- Created
-
2023-03-28Created from EPrint's datestamp field
- Updated
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2023-06-20Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering